Either the regions with black marks on Warcury’s body are more durable than the other non-black regions, or we can simply deduce that Luffy’s punch didn’t have ACOA and his AP was too weak to cause any damage with raw attack power alone, without ACOA.
Because Kaidou doesn’t take damage from physical blows no matter the strength behind them — even BG crashing down on Kaidou would be useless without internal destruction and ACoC. However, BG without any type of advanced Haki would still harm Warcury.
BG has much higher attack power than that, the gap is huge. Even with just basic Haki he would already be able to harm Warcury — to be honest, even without basic Haki he could, given the fact that Emeth managed to.